Nanoplastics (NPs) are emerging contaminants having persistent nature, diverse ecological impacts, and potential food safety risks. Here, we examined the ecotoxicity of 80 nm polystyrene nanoplastics (PS-NPs) at environmentally relevant concentrations (ERCs, 10 and 100 μg/L), and sublethal concentrations (SLCs, 500 and 2500 μg/L) in Magallana hongkongensis. Results showed that SLCs significantly (p < 0.05) increased superoxide dismutase (SOD), catalase (CAT), and alkaline phosphatase (AKP) activities and altered tnfα, cat, gst, sod, and se-gpx genetic expressions. Further, PS-NP exposure at both levels reduced beneficial bacteria and increased potentially pathogenic bacteria in the gut. In transcriptomic analysis, 5118 and 4180 differentially expressed genes (DEGs) were identified at ERCs, while 5665 and 4817 DEGs were found at SLCs, respectively. Upregulated DEGs enriched lysosomes, ABC transporters, and apoptosis pathways, while downregulated DEGs enriched ribosomal pathways. Overall, ERCs significantly altered gut microbiota and transcriptomic responses, while SLCs, in addition, also impacted the antioxidant and immune systems.